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Pythium aphanidermatum vs Pythium iwayamai LastZ results

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium aphanidermatum was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterPythium aphanidermatumPythium iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 39,530 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium aphanidermatum

Uncovered: 17,256,969 out of 35,876,849
Covered: 18,619,880 out of 35,876,849

Uncovered: 3,981,605 out of 18,015,574
Matches: 9,213,107 out of 18,015,574
Mismatches: 4,403,621 out of 18,015,574
Insertions: 417,241 out of 18,015,574
Identity over aligned base-pairs: 65.6%

Pythium iwayamai

Uncovered: 23,985,238 out of 43,199,174
Covered: 19,213,936 out of 43,199,174

Uncovered: 4,808,141 out of 19,552,457
Matches: 9,507,818 out of 19,552,457
Mismatches: 4,593,950 out of 19,552,457
Insertions: 642,548 out of 19,552,457
Identity over aligned base-pairs: 64.5%

Block size distribution

Size range All 39,530 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
139
735.0 bp
10 bp - 100 bp
4,188
280.7 kb
953
67.3 kb
100 bp - 1 kb
28,804
11.7 Mb
9,786
4.2 Mb
1 kb - 10 kb
6,387
10.8 Mb
6,012
16.0 Mb
10 kb - 100 kb
12
144.6 kb
187
2.7 Mb